From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Tue Mar 03 2009 - 21:07:54 CST
Why not just use catdcd to remove the waters? Just create an index
file listing the protein atoms that you want in your new dcd file and
then use the -i flag. You can create the index file by selecting the
protein atoms from your original pdb file:
set A [atomselect $molid "protein"]
$A get index
where $molid is whatever the molid is in vmd for where you loaded in
the pdb file. and then just cut and paste the output into a file.
As far as your original question goes, it sounds like you didn't
define the variable nf, so vmd doesn't know what to do.You should
probably take a look at a simple tcl tutorial if you are unclear about
tcl basics.
http://ctbp.ucsd.edu/summer_workshop04/01-vmd-tutorial/html/node3.html
Good luck.
Josh
On Mar 3, 2009, at 6:36 PM, jose correa wrote:
> Dear NAMD users
> I have a big *dcd file (10 GB), then, i can not open it in vmd,
> looking about the same problems, i applied the next scrip that was
> suggested in this forum, however, after run it in vmd Tk console
> show: can not read "nf" no such variable, unable to load structure
> file dry_prot.psf, can not reat nf" no such variable, invalid
> command. Any suggestion?, please.
> mol load psf solvated.psf
> for {set i 0 } {$i < $nf } {incr i 100 } {
> animate read dcd md0001.dcd beg i end i
> set sel [atomselect top protein]
> $sel writepdb $i.pdb
> if { $i == 0 } {
> $sel writepsf dry_prot.psf
> }
> $sel delete
> animate delete all
> }
> mol delete top
> mol load psf dry_prot.psf
> for {set i 0 } {$i < $nf } {incr i 100 } {
> animate read pdb $i.pdb
> file delete $i.pdb
> }
> animate write dcd {myprotein_prot.dcd} waitfor all
>
>
>
> best wishes
>
> j correa-basurto
>
>
>
>
------------------------------------------------------------------------------------------------------
Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley http://nature.berkeley.edu/~jadelman
Berkeley, CA 94720 USA jadelman_at_berkeley.edu
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